The Nielsen Lab has developed several software packages including:

BALLET
ANGSD
nSL
ngsTools
ngsF
SweepFinder2
trueFS
codonbias
CodonRecSim
PATRI
IM and IMa
MDIV
BAMSE
Relate
MISAT
MCMC_IBDfinder
AssotesteR

Browse additional programs made available by the Center for Theoretical Evolutionary Genomics here.